From: Han Choe (hchoe_at_amc.seoul.kr)
Date: Thu Mar 04 2004 - 16:48:46 CST
Thanks a lot for figuring out the cause of the problem for me.
From: Tim Isgro [mailto:timisgro_at_ks.uiuc.edu]
Sent: Friday, March 05, 2004 4:57 AM
To: Han Choe
Subject: Re: namd-l: CP3-NH3 error
Your protein has proline as the first residue in each segment. Because
of proline's funny cyclic geometry, you need to patch those N-termini
with the PROP patch in the topology file (psfgen: first PROP). Without
the patch, those first nitrogens are of type NH3, which yielded your
original problem. The attched psfgen script works.
Also, the script you sent me explicitly patched the N and C termini
(first NTER; last CTER). Note that psfgen does this automatically for
the first and last protein residues in a segment. Finally, you should
also use alias ILE CD1 CD.
On Tue, 2 Mar 2004, Tim Isgro wrote:
> Hi Han,
> There are no parameters for a CP3-NH3 bond in the Charmm parameter
> files. Do the peptide segments contain any exotic residues for which
> parameters might not be defined?
> On Tue, 2 Mar 2004, Han Choe wrote:
> > Dear All,
> > I generated a PSF file of 4 peptide segments using VMD and ran a
> > molecular dynamics simulation using NAMD. But I got an error
> > message, read "CAN'T FIND BOND PARAMETERS FOR BOND CP3-NH3 IN
> > PARAMETER FILES". What'd be wrong?
> > Cheers,
> > Han
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